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Randy H's Projects

bcftools icon bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bwa icon bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

clade-finder icon clade-finder

Determines Y-Haplogroup Clade From Positive and Negative SNPs

extract23 icon extract23

Extract a simulated 23andMe (V3) style file from a Whole Genome BAM file

fastp icon fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

genomeprep icon genomeprep

To preprocess, quality control and prepare consumer DTC genomes for research

haplogrep-cmd icon haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

htslib icon htslib

C library for high-throughput sequencing data formats

mosdepth icon mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

pyliftover icon pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

samtools icon samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

snps icon snps

tools for reading, writing, merging, and remapping SNPs

yleaf icon yleaf

Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data

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